The GLA gene encodes alpha-galactosidase (GLA; EC 3.2.1.22), a lysosomal hydrolase.  In a patient with Fabry disease,  a 1066C>T transition in the GLA gene results in a substitution from Arginine to Tryptophan at position 356 of the protein.  The substitution results in an enzymatic defect that results in the accumulation of globotriaoslyceramide and related glycosphingolipids in the plasma and cellular lysosomes of vessels, nerves, tissues and other organs throughout the body.  The result is a systemic disease manifested as progressive renal failure, cardiac disease, cerebrovascular disease, and skin lesions.

This week, we analyze the 3D Structure of the GLA protein.  From NCBI, "Structure of Human Alpha-galactosidase [Hydrolase EC:3.2.1.22] 2013/2/12" was chosen as this was the most recently updated representative human model of the GLA enzyme.  The PDB (Protein Data Bank) ID for this structure is 1R46.

Using CN3D, the GLA enzyme, a homodimeric glycoprotein, is represented below.

One of the 2 molecules is then removed and the following is a space filling view of the alpha-galactosidase molecule with position 356 highlighted in yellow.  In the variant protein, Arginine is substituted by Tryptophan at position 356 of the protein structure resulting in deficient activity of the enzyme.

By zooming in within the Worms View of CN3D, the following representation of position 356 (highlighted in yellow) is illustrated. It is apparent that position 356 is located in a turn region within the molecule.

Last week, we evaluated the secondary structure and hydropathy of the GLA protein.  The Garnier-Robson method predicted that in the normal GLA protein, position 356 would be located in a Beta sheet whereas the Chou-Fasman method predicted that position 356 would be located in an alpha helix.  With regards to the evaluation of hydropathy, both the Kyte-Doolittle and the Hopp-Woods methods predicted that position 356 would be hydrophilic.  By creating the 3D model via CN3D, we see that neither the Garnier-Robson nor the Chou-Fasman alogorithm of the secondary structure of the GLA protein correctly predicted location of position 356 as the above illustration (worms view) depicts position 356 in a turn region. [The illustration below from Protean 3D also depicts position 356 (highlighted in blue)  in a turn region.]  However, the  Kyte-Doolittle and the Hopp-Woods algorithms for hydropathy created in DNASTAR's Protean 3D were correct in predicting the 3 dimensional location of position 356 of the GLA protein as hydrophilic as predicted in the space filling view above.